Package org.biopax.paxtools.query.wrapperL3

Class TemplateReactionWrapper

java.lang.Object

org.biopax.paxtools.query.model.AbstractNode

org.biopax.paxtools.query.wrapperL3.EventWrapper

org.biopax.paxtools.query.wrapperL3.TemplateReactionWrapper

All Implemented Interfaces:

GraphObject, Node

public class TemplateReactionWrapper
extends EventWrapper

Wrapper for TemplateReaction class.

Author:

Ozgun Babur

Field Summary

Fields inherited from class org.biopax.paxtools.query.model.AbstractNode

banned, downstream, downstreamInited, graph, lowerEquivalent, pathSign, upperEquivalent, upstream, upstreamInited

Fields inherited from interface org.biopax.paxtools.query.model.Node

NEGATIVE, NEUTRAL, POSITIVE

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	TemplateReactionWrapper(TemplateReaction tempReac, GraphL3 graph)	Constructor with the TemplateReaction and the owner graph.

Method Summary

Modifier and Type	Method	Description
protected void	addToDownstream(PhysicalEntity pe, Graph graph)	Binds the given PhysicalEntity to the downstream.
protected void	addToUpstream(BioPAXElement ele, Graph graph)	Binds the given element to the upstream.
String	getKey()	Uses RDF ID of TemplateReaction as key.
TemplateReaction	getTempReac()	Gets the wrapped TemplateReaction
void	initDownstream()	Binds to products.
void	initUpstream()	Binds to template and controllers.
boolean	isTranscription()	This is transcription.

Methods inherited from class org.biopax.paxtools.query.wrapperL3.EventWrapper

getLowerEquivalent, getSign, getUpperEquivalent, isBreadthNode, isUbique

Methods inherited from class org.biopax.paxtools.query.model.AbstractNode

clear, getBanned, getDownstream, getDownstreamNoInit, getGraph, getPathSign, getUpstream, getUpstreamNoInit, init, initBanned, setBanned, setPathSign

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

TemplateReactionWrapper

protected TemplateReactionWrapper(TemplateReaction tempReac,
 GraphL3 graph)

Constructor with the TemplateReaction and the owner graph.

Parameters:

tempReac - TemplateReaction to wrap

graph - Owner graph

Method Details

initUpstream

public void initUpstream()

Binds to template and controllers.

Overrides:

initUpstream in class AbstractNode

initDownstream

public void initDownstream()

Binds to products.

Overrides:

initDownstream in class AbstractNode

isTranscription

public boolean isTranscription()

This is transcription.

Specified by:

isTranscription in interface Node

Specified by:

isTranscription in class EventWrapper

Returns:

True

addToDownstream

protected void addToDownstream(PhysicalEntity pe,
 Graph graph)

Binds the given PhysicalEntity to the downstream.

Overrides:

addToDownstream in class EventWrapper

Parameters:

pe - PhysicalEntity to bind

graph - Owner graph

addToUpstream

protected void addToUpstream(BioPAXElement ele,
 Graph graph)

Binds the given element to the upstream.

Overrides:

addToUpstream in class EventWrapper

Parameters:

ele - Element to bind

graph - Owner graph

getKey

public String getKey()

Uses RDF ID of TemplateReaction as key.

Returns:

RDF ID of TemplateReaction

getTempReac

public TemplateReaction getTempReac()

Gets the wrapped TemplateReaction

Returns:

The wrapped TemplateReaction